Merge pull request richarddurbin#24 from mcshane/feature/version2

print pbwt version and command line (second try)

.gitignore

@@ -19,3 +19,6 @@ utils
 *.exe
 *.out
 *.app
+
+# Version file
+/version.h

makefile

@@ -5,6 +5,20 @@ HTSLIB = $(HTSDIR)/libhts.a
 
 all: pbwt
 
+PBWT_COMMIT_HASH = ""
+ifneq "$(wildcard .git)" ""
+PBWT_COMMIT_HASH = $(shell git describe --always --long --dirty | sed 's/^[0-9\.]*-*//')
+version.h: $(if $(wildcard version.h),$(if $(findstring "$(PBWT_COMMIT_HASH)",$(shell cat version.h)),,force))
+endif
+version.h:
+	echo '#define PBWT_COMMIT_HASH "$(PBWT_COMMIT_HASH)"' > $@
+
+force:
+
+.c.o:
+	gcc -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
+
+
 test:
 	./test/test.pl
 
@@ -16,7 +30,7 @@ pbwt:  $(PBWT_OBJS) utils
 autozygExtract: autozygExtract.o
 	gcc $(CFLAGS) -o autozygExtract autozygExtract.o utils.o $(HTSLIB) -lpthread -lz -lm
 
-pbwtMain.o: pbwtMain.c pbwt.h utils.h
+pbwtMain.o: pbwtMain.c version.h pbwt.h utils.h
 	gcc $(CFLAGS) -c pbwtMain.c
 
 pbwtCore.o: pbwtCore.c pbwt.h utils.h
@@ -72,7 +86,7 @@ utils.o: utils.c utils.h
 	gcc $(CFLAGS) -c utils.c
 
 clean:
-	rm -f *.o pbwt *~
+	rm -f *.o pbwt *~ version.h
 
-.PHONY: all test clean
+.PHONY: all test clean force
 

pbwt.h

@@ -23,7 +23,10 @@
 
 #include "utils.h"
 
-static int pbwtMajorVersion = 3, pbwtMinorVersion = 0 ;
+const static int pbwtMajorVersion = 3, pbwtMinorVersion = 0 ;
+
+const char *pbwtCommitHash(void);
+const char *pbwtHtslibVersionString(void);
 
 /* data types */
 

pbwtHtslib.c

@@ -16,6 +16,11 @@
 #include <htslib/synced_bcf_reader.h>
 #include <htslib/faidx.h>
 
+const char *pbwtHtslibVersionString(void)
+{
+    return hts_version();
+}
+
 static void readVcfSamples (PBWT *p, bcf_hdr_t *hr)
 {
   int i, k ;
@@ -229,8 +234,11 @@ void pbwtWriteVcf (PBWT *p, char *filename, char *referenceFasta, char *mode)
       bcf_hdr_printf(bcfHeader, "##contig=<ID=%s,length=%d>", p->chrom, 0x7fffffff);   // MAX_CSI_COOR
     }
   kstring_t str = {0,0,0} ;
-  ksprintf(&str, "##pbwtVersion=%d.%d+htslib-%s", 
-	   pbwtMajorVersion, pbwtMinorVersion, hts_version()) ;
+  ksprintf(&str, "##pbwtVersion=%d.%d%s%s+htslib-%s", pbwtMajorVersion, pbwtMinorVersion, 
+          strcmp(pbwtCommitHash(),"")==0 ? "" : "-", pbwtCommitHash(), pbwtHtslibVersionString()) ;
+  bcf_hdr_append(bcfHeader, str.s) ;
+  str.l = 0;
+  ksprintf(&str, "##pbwtCommand=pbwt %s", commandLine) ;
   bcf_hdr_append(bcfHeader, str.s) ;
   free(str.s) ;
   bcf_hdr_append(bcfHeader, "##INFO=<ID=AC,Number=A,Type=Integer,Description=\"Allele count in genotypes\">") ;

pbwtMain.c

@@ -22,6 +22,7 @@
  */
 
 #include "pbwt.h"
+#include "version.h"
 
 /*********************************************************/
 
@@ -166,6 +167,11 @@ static void recordCommandLine (int argc, char *argv[])
 #define FOPEN(name,mode)  if (!strcmp (argv[1], "-")) fp = !strcmp(mode,"r") ? stdin : stdout ; else if (!(fp = fopen (argv[1],mode))) die ("failed to open %s file", name, argv[1])
 #define FCLOSE if (strcmp(argv[1], "-")) fclose(fp)
 
+const char *pbwtCommitHash(void)
+{
+    return PBWT_COMMIT_HASH ;
+}
+
 int main (int argc, char *argv[])
 {
   FILE *fp ;
@@ -179,7 +185,11 @@ int main (int argc, char *argv[])
   recordCommandLine (argc, argv) ;
 
   if (!argc)			/* print help */
-    { fprintf (stderr, "Usage: pbwt [ -<command> [options]* ]+\n") ;
+    { fprintf (stderr, "Program: pbwt\n") ;
+      fprintf (stderr, "Version: %d.%d%s%s (using htslib %s)\n", pbwtMajorVersion, pbwtMinorVersion, 
+                       strcmp(pbwtCommitHash(),"")==0 ? "" : "-", pbwtCommitHash(), pbwtHtslibVersionString()) ;
+      fprintf (stderr, "Contact: Richard Durbin [[email protected]]\n") ;
+      fprintf (stderr, "Usage: pbwt [ -<command> [options]* ]+\n") ;
       fprintf (stderr, "Commands:\n") ;
       fprintf (stderr, "  -check                    do various checks\n") ;
       fprintf (stderr, "  -stats                    print stats depending on commands; writes to stdout\n") ;

test/test.pl

@@ -186,24 +186,24 @@ sub test_pbwt
 sub test_write_vcf
 {
     my ($opts,%args) = @_;
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/pbwt -read $$opts{tmp}/$args{in}.pbwt -readSites $$opts{tmp}/$args{in}.sites -writeVcf - 2>/dev/null | grep -v ^##pbwtVersion >$$opts{tmp}/$args{out}");
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/pbwt -read $$opts{tmp}/$args{in}.pbwt -readSites $$opts{tmp}/$args{in}.sites -writeVcfGz - 2>/dev/null | $$opts{bin}/pbwt -readVcfGT - -writeVcf - 2>/dev/null | grep -v ^##pbwtVersion >$$opts{tmp}/$args{out}");
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/pbwt -read $$opts{tmp}/$args{in}.pbwt -readSites $$opts{tmp}/$args{in}.sites -writeBcf - 2>/dev/null | $$opts{bin}/pbwt -readVcfGT - -writeVcf - 2>/dev/null | grep -v ^##pbwtVersion >$$opts{tmp}/$args{out}");
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/pbwt -read $$opts{tmp}/$args{in}.pbwt -readSites $$opts{tmp}/$args{in}.sites -writeBcfGz - 2>/dev/null | $$opts{bin}/pbwt -readVcfGT - -writeVcf - 2>/dev/null | grep -v ^##pbwtVersion >$$opts{tmp}/$args{out}");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/pbwt -read $$opts{tmp}/$args{in}.pbwt -readSites $$opts{tmp}/$args{in}.sites -writeVcf - 2>/dev/null | grep -v ^##pbwt >$$opts{tmp}/$args{out}");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/pbwt -read $$opts{tmp}/$args{in}.pbwt -readSites $$opts{tmp}/$args{in}.sites -writeVcfGz - 2>/dev/null | $$opts{bin}/pbwt -readVcfGT - -writeVcf - 2>/dev/null | grep -v ^##pbwt >$$opts{tmp}/$args{out}");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/pbwt -read $$opts{tmp}/$args{in}.pbwt -readSites $$opts{tmp}/$args{in}.sites -writeBcf - 2>/dev/null | $$opts{bin}/pbwt -readVcfGT - -writeVcf - 2>/dev/null | grep -v ^##pbwt >$$opts{tmp}/$args{out}");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/pbwt -read $$opts{tmp}/$args{in}.pbwt -readSites $$opts{tmp}/$args{in}.sites -writeBcfGz - 2>/dev/null | $$opts{bin}/pbwt -readVcfGT - -writeVcf - 2>/dev/null | grep -v ^##pbwt >$$opts{tmp}/$args{out}");
 }
 
 sub test_read_vcf_gt
 {
     my ($opts,%args) = @_;
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/pbwt -readVcfGT $$opts{path}/read.vcf -writeVcf - 2>/dev/null | grep -v ^##pbwtVersion >$$opts{tmp}/$args{out}");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/pbwt -readVcfGT $$opts{path}/read.vcf -writeVcf - 2>/dev/null | grep -v ^##pbwt >$$opts{tmp}/$args{out}");
 }
 
 sub test_pbwt_reference_impute
 {
     my ($opts,%args) = @_;
     # create reference panel pbwt
     cmd("$$opts{bin}/pbwt -readVcfGT $$opts{path}/$args{ref}.vcf -writeAll $$opts{tmp}/$args{ref} 2>/dev/null");
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/pbwt -readVcfGT $$opts{path}/$args{in}.vcf -referenceImpute $$opts{tmp}/$args{ref} -writeVcf - 2>/dev/null | grep -v ^##pbwtVersion > $$opts{tmp}/$args{out}");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/pbwt -readVcfGT $$opts{path}/$args{in}.vcf -referenceImpute $$opts{tmp}/$args{ref} -writeVcf - 2>/dev/null | grep -v ^##pbwt > $$opts{tmp}/$args{out}");
 }
 
 sub test_merge